Lightnews — Scholar-powered news

Sebastian Schönherr @sebschoenherr.bsky.social · Jun 24

This is what I need today.

Sebastian Schönherr @sebschoenherr.bsky.social · Mar 14

Last November, we migrated the Michigan Imputation Server (imputationserver.sph.umich.edu) to a new software stack, including Nextflow. After some turbulence, we are more and more returning to normal operations, processing around 800.000 full human genomes per month.

Michigan Imputation Server 2

imputationserver.sph.umich.edu

3

Sebastian Schönherr @sebschoenherr.bsky.social · Mar 6

Today @michaelmoor.bsky.social took a train from Zurich to Innsbruck to kick-off our new Faculty of "AI and Scientific Computing"! 🎉 He talked about LLMs and Medical AI Agents. Exciting science and great discussions! Thanks! More info about our faculty: aiscm.i-med.ac.at #ai #scientificcomputing

Faculty of AI and Scientific Computing in Medicine (AISCM) Medical University of Innsbruck

Faculty of AI and Scientific Computing in Medicine

aiscm.i-med.ac.at

1 2

Sebastian Schönherr @sebschoenherr.bsky.social · Jan 29

Silvia is excited, we are so excited. Follow Silvia for great science and great fun.

www.youtube.com/watch?v=8iwB...

Silvia Di Maio @silvidm.bsky.social · Jan 29

Our Nextflow in Genomics workshop kicks off tomorrow!
Excited to dive into imputation with @sebschoenherr.bsky.social and @lukfor.bsky.social

#nf-genomics #freeimputation

3

Sebastian Schönherr @sebschoenherr.bsky.social · Jan 29

🚀 Ready to kick off our Nextflow in Genomics workshop tomorrow at @i-med.ac.at!
🎉 Together with @lukfor.bsky.social & @silvidm.bsky.social we'll work on improving imputation server workflows.

Big thanks to @nextflow.io, @evanfloden.bsky.social, and @ewels.bsky.social for the support.

6

Sebastian Schönherr @sebschoenherr.bsky.social · Jan 21

If you didn't hear back from me today, it's because I had to solve a 4th grade math test first.

2

Sebastian Schönherr @sebschoenherr.bsky.social · Jan 16

Almost forgot: Shout out to @nextflow.io for sending us stickers to get a bit of conference vibe here in innsbruck 🎉

1

Sebastian Schönherr @sebschoenherr.bsky.social · Jan 16

Details about the workshop can be found here: genepi.i-med.ac.at/workshops/ne... Please feel free to reply directly to this thread for feature requests or via Github: github.com/genepi/imput...
2/2

Nextflow In Genomics 2025 - Genepi Innsbruck

Institute of Genetic Epidemiology, Medical University of Innsbruck

genepi.i-med.ac.at

3

Sebastian Schönherr @sebschoenherr.bsky.social · Jan 16

Are you working with one of the genotype imputation servers? Then this is your chance to see new features pretty soon on the server: @lukfor.bsky.social ky.social, @silvidm.bsky.social, and I are hosting our 2nd Nextflow in Genomics Hackathon to boost imputation servers here @i-med.ac.at
1/2

Nextflow In Genomics 2025 - Genepi Innsbruck

Institute of Genetic Epidemiology, Medical University of Innsbruck

genepi.i-med.ac.at

2 4 10

Reposted by Sebastian Schönherr

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 28

Publishing software is often easier than maintaining it - but we’re committed to keeping ours up to date! 🛠️ We've enhanced the documentation for our mtDNA variant calling pipeline, with detailed guides for both graphical and command-line use with Nextflow:
mitoverse.readthedocs.io/mtdna-server...

mtDNA-Server 2 - Mitoverse

mitoverse.readthedocs.io

1 4 6

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 28

Btw, you can now set the mean minimum coverage when submitting a job, making it easier to work with low-coverage data. Let us know which features you’d like to see next. For graphical job execution click here: mitoverse.i-med.ac.at

mitoverse

mitoverse.i-med.ac.at

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 28

Publishing software is often easier than maintaining it - but we’re committed to keeping ours up to date! 🛠️ We've enhanced the documentation for our mtDNA variant calling pipeline, with detailed guides for both graphical and command-line use with Nextflow:
mitoverse.readthedocs.io/mtdna-server...

mtDNA-Server 2 - Mitoverse

mitoverse.readthedocs.io

1 4 6

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 27

endless slopes

4

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 19

And I almost forgot the most frightening moment in this journey: shutting down the old server after 9 years. #byebyehadoop

2

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 19

Our framework AND pipeline are now used by all the major imputation servers - Michigan, Topmed, Munich - which makes us quite proud. It’s also great to see @stephenturner.us covering us in his recent blog: tinyurl.com/5tp9tz7e.
We would love to hear from more imputation servers around the world. 🌏

2 4

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 19

This summer, @lukfor.bsky.social and I migrated the Michigan Imputation Server to Nextflow. 2M genomes later, we can say it was a big success.

As a Christmas gift, we’re excited to show you how to set up your own local server in under 10 minutes.

##freeimputation

genepi.github.io/michigan-imp...

2 5 11

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 16

Last week was fun! We had the pleasure of welcoming a MINT high school to our institute to talk about A.I 🤖. We also dived into Genetics (by @stncsn.bsky.social), Medicine, and discussed their project on AI-powered shark detection. 🧬🩺🦈 #STEM #MINT #Education #AI #Genetics @meduniibk.bsky.social

4

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 13

Today @silvidm.bsky.social delivered an impressive talk on her latest research on repetitive regions in the human genome - could they hold the key to the missing heritability? Huge thanks to the Biocenter @meduniibk.bsky.social for hosting this. #ukb #nextflow #lpa #vntrs

2 5

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 5

We believe this work will help others analyze VNTRs from short-read sequencing data and understand their impact on numerous human phenotypes, potentially explaining parts of the missing heritability. end.

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 5

For the first time, we were able to analyze the LPA VNTR in >199,000 samples from the UKB. This approach successfully revealed new, strong Lp(a)-lowering effects for KIV-2 variants, with a protective effect against coronary artery disease, and also validated previous findings. 5/n

1

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 5

And yes, we can! We developed a computational approach to resolve intra-repeat variation in the KIV-2 VNTR region using widely available short-read sequencing data, and we also applied it to 5 other medically relevant VNTRs 4/n

1

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 5

We specifically focused on the "dark" region of the cardiovascular disease gene LPA – the so-called KIV-2 VNTR. We wanted to determine if we could decipher this region using short-read sequencing data 3/n

1

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 5

In July this year, we (Silvia Di Maio, Peter Zöscher and @stncsn.bsky.social et al.) published a Genome Biology paper to decipher repeats in the human genome, so called VNTRs genomebiology.biomedcentral.com/articles/10.... 2/n

Resolving intra-repeat variation in medically relevant VNTRs from short-read sequencing data using the cardiovascular risk gene LPA as a model - Genome Biology

Background Variable number tandem repeats (VNTRs) are highly polymorphic DNA regions harboring many potentially disease-causing variants. However, VNTRs often appear unresolved (“dark”) in variation d...

genomebiology.biomedcentral.com

1 1

Sebastian Schönherr @sebschoenherr.bsky.social · Dec 5

A typical shot from my life as a researcher at @meduniibk.bsky.social. Standing in the HPC center with Silvia Di Maio and looking at dark genome regions

What's the story behind? 1/n

(c) Medical University of Innsbruck, Cristof Simon

1 1 8

Sebastian Schönherr @sebschoenherr.bsky.social · Nov 25

🌍 The imputation servers running on our software stack:

🛰️ Our Main Instance: imputationserver.sph.umich.edu
🛰️ TOPMed: imputation.biodatacatalyst.nhlbi.nih.gov
🛰️ MUC: imputationserver.helmholtz-munich.de

💡 Are there other imputation servers flying around?

1 1